Wills describes himself as a Roman Catholic and, with the exception of a period of doubt during his seminary years, has been a Roman Catholic all his life.[8] He continues to attend Mass at the Sheil Catholic Center in Northwestern University. He prays the rosary every day, and wrote a book about the devotion (The Rosary: Prayer Comes Around) in 2005.[9]

Wills published a full-length analysis of the contemporary Catholic Church, Bare Ruined Choirs, in 1972 and a full-scale criticism of the historical and contemporary church, Papal Sin: Structures of Deceit, in 2000. He followed up the latter with a sequel, Why I Am a Catholic (2002), as well as with the books What Jesus Meant (2006), What Paul Meant (2006), and What the Gospels Meant (2008).

Wills began his career as an early protégé of William F. Buckley Jr. and was associated with conservatism. When he first became involved with National Review he did not know if he was a conservative, calling himself a distributionist.[14] Later on, he was self-admittedly conservative, being regarded for a time as the "token conservative" for the National Catholic Reporter and even writing a book entitled Confessions of a Conservative.[9]

In 1995, Wills wrote an article about the Second Amendment for The New York Review of Books. Originally entitled "Why We Have No Right to Bear Arms", that was not Wills's contention and he neither wrote the title nor approved it prior to the article's publication.[17] Instead, Wills argued that the Second Amendment does not justify private ownership of guns but rather refers to the right to keep and bear arms in a military context only. Furthermore, that military context does not entail the right to overthrow the government of the United States:

The Standard Model finds, squirrelled away in the Second Amendment, not only a private right to own guns for any purpose but a public right to oppose with arms the government of the United States. It grounds this claim in the right of insurrection, which clearly does exist whenever tyranny exists. Yet the right to overthrow the government is not given by government. It arises when government no longer has any authority. One cannot say one rebels by right of that nonexistent authority. Modern militias say the government itself instructs them to overthrow government – and wacky scholars endorse this view. They think the Constitution is so deranged a document that it brands as the greatest crime a war upon itself (in Article III: 'Treason against the United States shall consist only in levying war against them...') and then instructs its citizens to take this up (in the Second Amendment). According to this doctrine, a well-regulated group is meant to overthrow its own regulator, and a soldier swearing to obey orders is disqualified from true militia virtue.[18]

Gary Wills was inducted as a Laureate of The Lincoln Academy of Illinois and awarded the Order of Lincoln (the State’s highest honor) by the Governor of Illinois in 2006 in the area of Communication and Education.[25]

^John B. Judis (1990). William F. Buckley, Jr.: Patron Saint of the Conservatives. Simon & Schuster. p. 158. ISBN0-671-69593-2. Wills ... did not know whether he was a conservative (he called himself a 'distributionist')

^"'To Keep and Bear Arms: An Exchange'". New York Review of Books. November 16, 1995. 'I had no knowledge of the misleading cover title "Why We Have No Right to Bear Arms" before I read with dismay the printed issue. Of course the Amendment states a right that "we" do possess – but we possess it, as the Amendment itself says, in a "well-regulated militia."